https://wiki.pagelibre.org/ 2026-05-06T02:56:19+00:00 https://wiki.pagelibre.org/ https://wiki.pagelibre.org/lib/tpl/dokuwiki/images/favicon.ico text/html 2021-04-08T11:52:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.pagelibre.org/doku.php?id=bioinfo:bwa&rev=1617875573&do=diff Here we will use the BWA aligner to map short reads to a reference genome, and then call variants (differences between the reads and the reference). Download data Goal: get the sequence data! Run: mkdir ~/data cd ~/data curl -O http://dib-training.ucdavis.edu.s3.amazonaws.com/2017-ucdavis-igg201b/SRR2584857.fq.gz text/html 2023-09-12T23:15:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.pagelibre.org/doku.php?id=bioinfo:oneliners&rev=1694553334&do=diff for filename in *.fa; do sed -i '/>Recurrent fasta name/c\>'$filename'' $filename; done all VCF to vcf.gz ls *.vcf | xargs -n1 -P0 bgzip AWK awk '{if(NR%4==2) {count++; bases += length} } END{print bases/count}' <fastq_file> # keep online lines with col 5 & 4 of length == 1char zgrep -v "\.\/\.:\." Merged.vcf.gz | awk '{if (length($5)==1 && length($4)==1) print $line}'